Starting phenix.real_space_refine on Thu Mar 21 18:34:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8c_43034/03_2024/8v8c_43034_trim_updated.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 S 113 5.16 5 Cl 10 4.86 5 C 10182 2.51 5 N 2483 2.21 5 O 2828 1.98 5 H 15011 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 9": "OE1" <-> "OE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "E GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30630 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 5975 Classifications: {'peptide': 373} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 352} Chain breaks: 1 Chain: "B" Number of atoms: 5997 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5984 Classifications: {'peptide': 374} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 353} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 374, 5985 Classifications: {'peptide': 374} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 353} Chain breaks: 1 bond proxies already assigned to first conformer: 6055 Chain: "C" Number of atoms: 6060 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 6047 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 6048 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 bond proxies already assigned to first conformer: 6118 Chain: "D" Number of atoms: 6080 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 6067 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 378, 6068 Classifications: {'peptide': 378} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 357} Chain breaks: 1 bond proxies already assigned to first conformer: 6139 Chain: "E" Number of atoms: 6060 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 377, 6047 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 377, 6048 Classifications: {'peptide': 377} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 bond proxies already assigned to first conformer: 6118 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 64 Unusual residues: {' CA': 1, 'EPJ': 1, 'I34': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'EPJ': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 84 Unusual residues: {'EPJ': 1, 'I34': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 21.28, per 1000 atoms: 0.69 Number of scatterers: 30630 At special positions: 0 Unit cell: (89.925, 91.575, 146.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 Cl 10 17.00 S 113 16.00 O 2828 8.00 N 2483 7.00 C 10182 6.00 H 15011 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.02 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.08 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 601 " - " ASN A 67 " " NAG A 602 " - " ASN A 23 " " NAG B 602 " - " ASN B 67 " " NAG B 603 " - " ASN B 23 " " NAG C 602 " - " ASN C 67 " " NAG C 603 " - " ASN C 23 " " NAG D 602 " - " ASN D 67 " " NAG D 603 " - " ASN D 23 " " NAG E 602 " - " ASN E 67 " " NAG E 603 " - " ASN E 23 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN B 110 " " NAG H 1 " - " ASN C 110 " " NAG I 1 " - " ASN D 110 " " NAG J 1 " - " ASN E 110 " Time building additional restraints: 25.74 Conformation dependent library (CDL) restraints added in 5.0 seconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3586 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 25 sheets defined 37.4% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.817A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.523A pdb=" N LEU A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 259 Processing helix chain 'A' and resid 269 through 295 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 429 through 465 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 230 removed outlier: 4.203A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 259 removed outlier: 3.629A pdb=" N THR B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 295 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 426 through 466 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 229 removed outlier: 4.191A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 257 removed outlier: 3.559A pdb=" N GLY C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 295 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 426 through 465 Processing helix chain 'C' and resid 470 through 477 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 68 through 70 No H-bonds generated for 'chain 'D' and resid 68 through 70' Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 230 removed outlier: 3.561A pdb=" N VAL D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 238 through 248 Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 269 through 295 Processing helix chain 'D' and resid 308 through 311 No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 425 through 466 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 216 through 229 removed outlier: 4.149A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 238 through 249 Processing helix chain 'E' and resid 251 through 258 Processing helix chain 'E' and resid 269 through 295 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 426 through 466 removed outlier: 3.568A pdb=" N GLU E 431 " --> pdb=" O GLN E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 477 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 5.995A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 Processing sheet with id= C, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.641A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 177 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU A 175 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.126A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= H, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= J, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.637A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU B 175 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.296A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= O, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.542A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 177 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU C 175 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.125A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= R, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= S, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= T, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.694A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 177 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU D 175 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.309A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= W, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= X, first strand: chain 'E' and resid 76 through 79 Processing sheet with id= Y, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.575A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY E 177 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.00 Time building geometry restraints manager: 26.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4871 1.04 - 1.24: 12138 1.24 - 1.45: 5140 1.45 - 1.65: 8750 1.65 - 1.85: 177 Bond restraints: 31076 Sorted by residual: bond pdb=" C3 EPJ A 603 " pdb=" N1 EPJ A 603 " ideal model delta sigma weight residual 1.718 1.463 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C3 EPJ E 604 " pdb=" N1 EPJ E 604 " ideal model delta sigma weight residual 1.718 1.469 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C3 EPJ B 604 " pdb=" N1 EPJ B 604 " ideal model delta sigma weight residual 1.718 1.469 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C3 EPJ D 604 " pdb=" N1 EPJ D 604 " ideal model delta sigma weight residual 1.718 1.471 0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C3 EPJ C 604 " pdb=" N1 EPJ C 604 " ideal model delta sigma weight residual 1.718 1.471 0.247 2.00e-02 2.50e+03 1.53e+02 ... (remaining 31071 not shown) Histogram of bond angle deviations from ideal: 93.69 - 105.94: 840 105.94 - 118.19: 40492 118.19 - 130.44: 14570 130.44 - 142.68: 112 142.68 - 154.93: 2 Bond angle restraints: 56016 Sorted by residual: angle pdb=" CA PHE D 424 " pdb=" N PHE D 424 " pdb=" H PHE D 424 " ideal model delta sigma weight residual 114.00 154.93 -40.93 3.00e+00 1.11e-01 1.86e+02 angle pdb=" CA ASP A 428 " pdb=" N ASP A 428 " pdb=" H ASP A 428 " ideal model delta sigma weight residual 114.00 151.60 -37.60 3.00e+00 1.11e-01 1.57e+02 angle pdb=" N LEU E 249 " pdb=" CA LEU E 249 " pdb=" C LEU E 249 " ideal model delta sigma weight residual 113.18 104.59 8.59 1.21e+00 6.83e-01 5.04e+01 angle pdb=" C SER C 149 " pdb=" CA SER C 149 " pdb=" CB SER C 149 " ideal model delta sigma weight residual 109.38 118.04 -8.66 1.68e+00 3.54e-01 2.66e+01 angle pdb=" N LEU D 247 " pdb=" CA LEU D 247 " pdb=" C LEU D 247 " ideal model delta sigma weight residual 112.90 107.26 5.64 1.31e+00 5.83e-01 1.85e+01 ... (remaining 56011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 13759 17.66 - 35.33: 896 35.33 - 52.99: 260 52.99 - 70.65: 66 70.65 - 88.32: 16 Dihedral angle restraints: 14997 sinusoidal: 8148 harmonic: 6849 Sorted by residual: dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual 180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual -180.00 -152.51 -27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 14994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2249 0.090 - 0.180: 233 0.180 - 0.269: 12 0.269 - 0.359: 7 0.359 - 0.449: 2 Chirality restraints: 2503 Sorted by residual: chirality pdb=" CB VAL E 256 " pdb=" CA VAL E 256 " pdb=" CG1 VAL E 256 " pdb=" CG2 VAL E 256 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA SER C 149 " pdb=" N SER C 149 " pdb=" C SER C 149 " pdb=" CB SER C 149 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA SER D 149 " pdb=" N SER D 149 " pdb=" C SER D 149 " pdb=" CB SER D 149 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 2500 not shown) Planarity restraints: 4465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " 0.342 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG E 602 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " 0.132 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.332 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG A 601 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.506 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 213 " -0.128 2.00e-02 2.50e+03 1.38e-01 2.87e+02 pdb=" CG ASN B 213 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 213 " 0.124 2.00e-02 2.50e+03 pdb=" ND2 ASN B 213 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN B 213 " 0.202 2.00e-02 2.50e+03 pdb="HD22 ASN B 213 " -0.205 2.00e-02 2.50e+03 ... (remaining 4462 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 494 2.01 - 2.66: 40101 2.66 - 3.30: 89211 3.30 - 3.95: 120076 3.95 - 4.60: 183526 Nonbonded interactions: 433408 Sorted by model distance: nonbonded pdb=" HE2 TYR D 209 " pdb=" HE1 TYR D 210 " model vdw 1.362 2.100 nonbonded pdb="HD11 LEU C 215 " pdb="HD21 LEU C 464 " model vdw 1.410 2.440 nonbonded pdb="HG22 ILE A 221 " pdb="HG13 VAL A 245 " model vdw 1.421 2.440 nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.425 2.100 nonbonded pdb="HD12 LEU B 231 " pdb=" HD2 PRO B 232 " model vdw 1.433 2.440 ... (remaining 433403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 113 or resid 115 through 321 or resid 428 throug \ h 478 or resid 602)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 425 or resid 428 throug \ h 478 or resid 602)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 321 or resid 428 throug \ h 478 or resid 602)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 321 or resid 428 throug \ h 478 or resid 602)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 321 or resid 428 throug \ h 478 or resid 602)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.440 Extract box with map and model: 9.770 Check model and map are aligned: 0.430 Set scattering table: 0.290 Process input model: 107.670 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.255 16065 Z= 0.737 Angle : 1.091 10.609 21907 Z= 0.564 Chirality : 0.059 0.449 2503 Planarity : 0.011 0.295 2685 Dihedral : 13.744 88.318 6052 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.18), residues: 1863 helix: -0.83 (0.18), residues: 701 sheet: -1.29 (0.22), residues: 453 loop : -1.16 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 307 HIS 0.006 0.001 HIS C 297 PHE 0.022 0.002 PHE E 134 TYR 0.031 0.003 TYR D 209 ARG 0.021 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 315 TRP cc_start: 0.7042 (m-10) cc_final: 0.6523 (t60) REVERT: E 253 MET cc_start: 0.6716 (tpt) cc_final: 0.6368 (tpt) outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 0.6006 time to fit residues: 227.2533 Evaluate side-chains 191 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 16065 Z= 0.202 Angle : 0.588 6.774 21907 Z= 0.303 Chirality : 0.041 0.187 2503 Planarity : 0.005 0.062 2685 Dihedral : 8.125 88.146 2502 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.88 % Allowed : 4.76 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1863 helix: 0.29 (0.19), residues: 702 sheet: -1.20 (0.22), residues: 449 loop : -0.88 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 307 HIS 0.004 0.001 HIS E 295 PHE 0.018 0.001 PHE E 319 TYR 0.015 0.001 TYR C 209 ARG 0.003 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6687 (mt-10) REVERT: B 315 TRP cc_start: 0.7013 (m-10) cc_final: 0.6585 (t60) REVERT: E 231 LEU cc_start: 0.8475 (mp) cc_final: 0.8122 (mp) REVERT: E 253 MET cc_start: 0.6234 (tpt) cc_final: 0.5649 (tpt) outliers start: 15 outliers final: 14 residues processed: 212 average time/residue: 0.5575 time to fit residues: 179.7657 Evaluate side-chains 198 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 443 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 ASN C 47 GLN E 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 16065 Z= 0.410 Angle : 0.635 5.876 21907 Z= 0.331 Chirality : 0.043 0.175 2503 Planarity : 0.005 0.060 2685 Dihedral : 7.854 87.980 2502 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.35 % Allowed : 5.34 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1863 helix: 0.49 (0.19), residues: 705 sheet: -1.27 (0.22), residues: 455 loop : -0.85 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 307 HIS 0.009 0.001 HIS E 295 PHE 0.026 0.002 PHE E 134 TYR 0.027 0.002 TYR E 209 ARG 0.004 0.001 ARG E 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6811 (mt-10) REVERT: A 461 ILE cc_start: 0.8183 (mt) cc_final: 0.7705 (pt) REVERT: B 61 ASP cc_start: 0.7427 (t0) cc_final: 0.7145 (t0) REVERT: B 315 TRP cc_start: 0.7142 (m-10) cc_final: 0.6686 (t60) REVERT: C 465 MET cc_start: 0.7225 (ttp) cc_final: 0.6912 (mtp) REVERT: E 231 LEU cc_start: 0.8498 (mp) cc_final: 0.8220 (mp) outliers start: 23 outliers final: 21 residues processed: 204 average time/residue: 0.5732 time to fit residues: 176.5293 Evaluate side-chains 200 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16065 Z= 0.284 Angle : 0.562 5.606 21907 Z= 0.291 Chirality : 0.041 0.156 2503 Planarity : 0.004 0.060 2685 Dihedral : 7.589 89.949 2502 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.00 % Allowed : 6.58 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1863 helix: 0.70 (0.19), residues: 706 sheet: -1.21 (0.23), residues: 448 loop : -0.81 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 307 HIS 0.005 0.001 HIS E 295 PHE 0.022 0.001 PHE E 319 TYR 0.020 0.001 TYR D 209 ARG 0.003 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 ILE cc_start: 0.7749 (mm) cc_final: 0.7502 (mm) REVERT: A 461 ILE cc_start: 0.8164 (mt) cc_final: 0.7667 (pt) REVERT: B 61 ASP cc_start: 0.7365 (t0) cc_final: 0.7097 (t0) REVERT: B 315 TRP cc_start: 0.7181 (m-10) cc_final: 0.6682 (t60) REVERT: E 231 LEU cc_start: 0.8499 (mp) cc_final: 0.8245 (mp) outliers start: 17 outliers final: 14 residues processed: 198 average time/residue: 0.5794 time to fit residues: 174.4034 Evaluate side-chains 191 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 152 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 0.0040 chunk 160 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16065 Z= 0.149 Angle : 0.496 5.424 21907 Z= 0.254 Chirality : 0.039 0.157 2503 Planarity : 0.004 0.055 2685 Dihedral : 7.079 85.442 2502 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.82 % Allowed : 6.69 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1863 helix: 1.07 (0.19), residues: 709 sheet: -1.14 (0.23), residues: 460 loop : -0.52 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 307 HIS 0.003 0.001 HIS B 295 PHE 0.025 0.001 PHE E 319 TYR 0.015 0.001 TYR D 209 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8030 (mt) cc_final: 0.7536 (pt) REVERT: B 61 ASP cc_start: 0.7352 (t0) cc_final: 0.7063 (t0) REVERT: B 315 TRP cc_start: 0.7148 (m-10) cc_final: 0.6647 (t60) REVERT: E 231 LEU cc_start: 0.8422 (mp) cc_final: 0.8198 (mp) outliers start: 14 outliers final: 11 residues processed: 199 average time/residue: 0.5960 time to fit residues: 177.9143 Evaluate side-chains 188 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.0670 chunk 161 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 0.0370 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16065 Z= 0.143 Angle : 0.481 5.520 21907 Z= 0.246 Chirality : 0.039 0.162 2503 Planarity : 0.004 0.061 2685 Dihedral : 6.884 84.209 2502 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.76 % Allowed : 6.81 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 1863 helix: 1.23 (0.19), residues: 705 sheet: -1.04 (0.23), residues: 461 loop : -0.34 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 307 HIS 0.002 0.000 HIS B 295 PHE 0.008 0.001 PHE E 134 TYR 0.018 0.001 TYR E 209 ARG 0.004 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 186 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 ILE cc_start: 0.8041 (mt) cc_final: 0.7551 (pt) REVERT: B 61 ASP cc_start: 0.7350 (t0) cc_final: 0.7057 (t0) REVERT: B 315 TRP cc_start: 0.7166 (m-10) cc_final: 0.6642 (t60) REVERT: E 231 LEU cc_start: 0.8392 (mp) cc_final: 0.8154 (mp) outliers start: 13 outliers final: 11 residues processed: 194 average time/residue: 0.5621 time to fit residues: 166.1314 Evaluate side-chains 188 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 150 optimal weight: 0.0980 chunk 99 optimal weight: 6.9990 chunk 178 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.0570 chunk 110 optimal weight: 0.3980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 16065 Z= 0.140 Angle : 0.476 6.580 21907 Z= 0.243 Chirality : 0.039 0.153 2503 Planarity : 0.004 0.053 2685 Dihedral : 6.675 83.528 2502 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.82 % Allowed : 7.11 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1863 helix: 1.40 (0.19), residues: 703 sheet: -1.02 (0.23), residues: 454 loop : -0.23 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 307 HIS 0.003 0.000 HIS B 295 PHE 0.009 0.001 PHE E 319 TYR 0.014 0.001 TYR A 209 ARG 0.002 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 VAL cc_start: 0.8278 (t) cc_final: 0.8045 (t) REVERT: A 461 ILE cc_start: 0.8050 (mt) cc_final: 0.7558 (pt) REVERT: B 61 ASP cc_start: 0.7366 (t0) cc_final: 0.7082 (t0) REVERT: B 315 TRP cc_start: 0.7155 (m-10) cc_final: 0.6600 (t60) REVERT: E 231 LEU cc_start: 0.8359 (mp) cc_final: 0.8137 (mp) outliers start: 14 outliers final: 11 residues processed: 198 average time/residue: 0.5926 time to fit residues: 178.7957 Evaluate side-chains 192 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 181 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 121 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16065 Z= 0.303 Angle : 0.543 5.933 21907 Z= 0.280 Chirality : 0.040 0.146 2503 Planarity : 0.004 0.054 2685 Dihedral : 6.995 85.858 2502 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.76 % Allowed : 7.57 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.19), residues: 1863 helix: 1.20 (0.19), residues: 719 sheet: -1.10 (0.23), residues: 445 loop : -0.29 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 307 HIS 0.005 0.001 HIS E 295 PHE 0.022 0.001 PHE E 134 TYR 0.014 0.001 TYR A 209 ARG 0.003 0.001 ARG C 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 VAL cc_start: 0.8373 (t) cc_final: 0.8151 (t) REVERT: A 461 ILE cc_start: 0.8058 (mt) cc_final: 0.7554 (pt) REVERT: B 315 TRP cc_start: 0.7159 (m-10) cc_final: 0.6604 (t60) outliers start: 13 outliers final: 12 residues processed: 192 average time/residue: 0.5696 time to fit residues: 165.1782 Evaluate side-chains 189 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 177 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 100 optimal weight: 0.0030 chunk 72 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16065 Z= 0.146 Angle : 0.486 5.919 21907 Z= 0.248 Chirality : 0.039 0.148 2503 Planarity : 0.004 0.053 2685 Dihedral : 6.718 86.059 2502 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.53 % Allowed : 7.69 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1863 helix: 1.46 (0.19), residues: 705 sheet: -1.07 (0.24), residues: 444 loop : -0.19 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 307 HIS 0.003 0.000 HIS B 295 PHE 0.008 0.001 PHE E 439 TYR 0.014 0.001 TYR A 209 ARG 0.003 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 181 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 VAL cc_start: 0.8269 (t) cc_final: 0.8037 (t) REVERT: A 461 ILE cc_start: 0.8013 (mt) cc_final: 0.7505 (pt) REVERT: B 315 TRP cc_start: 0.7131 (m-10) cc_final: 0.6654 (t60) REVERT: D 465 MET cc_start: 0.7063 (mtp) cc_final: 0.6787 (mtp) outliers start: 9 outliers final: 9 residues processed: 190 average time/residue: 0.5677 time to fit residues: 164.0587 Evaluate side-chains 187 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 113 optimal weight: 0.0470 chunk 89 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16065 Z= 0.187 Angle : 0.492 6.108 21907 Z= 0.252 Chirality : 0.039 0.143 2503 Planarity : 0.004 0.053 2685 Dihedral : 6.673 85.874 2502 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.65 % Allowed : 7.57 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.20), residues: 1863 helix: 1.51 (0.19), residues: 705 sheet: -1.08 (0.23), residues: 446 loop : -0.15 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.003 0.001 HIS E 295 PHE 0.016 0.001 PHE E 252 TYR 0.018 0.001 TYR A 209 ARG 0.002 0.000 ARG B 204 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 VAL cc_start: 0.8290 (t) cc_final: 0.8059 (t) REVERT: A 461 ILE cc_start: 0.7965 (mt) cc_final: 0.7478 (pt) REVERT: B 315 TRP cc_start: 0.7134 (m-10) cc_final: 0.6651 (t60) REVERT: C 43 ASP cc_start: 0.7808 (t70) cc_final: 0.7261 (t0) REVERT: C 46 ASN cc_start: 0.8697 (m-40) cc_final: 0.8470 (m110) outliers start: 11 outliers final: 11 residues processed: 191 average time/residue: 0.6389 time to fit residues: 188.8289 Evaluate side-chains 193 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 227 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 150 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.117388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104135 restraints weight = 101096.910| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.33 r_work: 0.3520 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16065 Z= 0.247 Angle : 0.520 5.739 21907 Z= 0.269 Chirality : 0.039 0.164 2503 Planarity : 0.004 0.054 2685 Dihedral : 6.807 87.353 2502 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.70 % Allowed : 7.57 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.20), residues: 1863 helix: 1.37 (0.19), residues: 717 sheet: -1.09 (0.24), residues: 439 loop : -0.19 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 307 HIS 0.004 0.001 HIS E 295 PHE 0.018 0.001 PHE E 134 TYR 0.012 0.001 TYR A 209 ARG 0.002 0.000 ARG B 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6540.69 seconds wall clock time: 115 minutes 51.54 seconds (6951.54 seconds total)